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| Status |
Public on Jun 12, 2017 |
| Title |
Genome-wide primary transcriptome landscape reveals the diversity of regulatory elements in archaeal genomes |
| Organism |
Thermococcus onnurineus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We show the transcriptomic landscape of the H2-producing archaeon Thermococcus onnurineus NA1 in response to different growth conditions using primary and whole transcriptome sequencing. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA boxes, A-rich B recognition elements (BREs), and promoter proximal element (PPE) motifs in promoter regions, a high pyrimidine nucleotide content (T/C) at the −1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs). In addition, along with differential transcript levels, 117 leaderless genes and 86 non-coding RNAs (ncRNAs) were identified, representing diverse cellular functions and potential regulatory functions during hydrogen production. Further comparative analysis of T. onnurineus upstream regulatory sequences with those of closely related archaeal genomes demonstrated that orthologous genes are expressed from highly conserved promoter sequences, however their upstream sequences for transcriptional and translational regulation are largely diverse. This study suggests that closely related archaea maintain orthologous gene functions, but may diversify the elements that regulate them to adapt to their unique environmental habitats.
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| Overall design |
Profiles of primary transcripts and whole transcripts of Thermococcus onnurineus NA1 were generated by deep sequencing using Illumina Miseq and Illumina Genome Analyzer IIx.
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| Contributor(s) |
Cho S, Kim M, Jeong Y, Lee B, Lee J, Kang SG, Cho B |
| Citation(s) |
28216628 |
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| Submission date |
Aug 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yujin Jeong |
| E-mail(s) |
dbwls54@gmail.com
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| Organization name |
KAIST
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| Street address |
291 Daehak-ro
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platforms (2) |
| GPL22336 |
Illumina MiSeq (Thermococcus onnurineus) |
| GPL22337 |
Illumina Genome Analyzer IIx (Thermococcus onnurineus) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA339284 |
| SRA |
SRP082373 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE85760_RAW.tar |
90.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE85760_TSS_processed.txt.gz |
9.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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